Research workbench
Plasmodium falciparum dutpase in complex with a trityl ligand
Analyse Plasmodium falciparum dutpase in complex with a trityl ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y8C
- Type
- protein
- Length
- 404 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyuridine 5'-triphosphate nucleotidohydrolase
- EC
- 3.6.1.23
- UniProt
- Q8II92
- Ligands
- DUQ, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 145 | 9% helix, 40% strand | Q8II92 |
| B | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 123 | 11% helix, 46% strand | Q8II92 |
| C | Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) | protein | 136 | 10% helix, 43% strand | Q8II92 |
Ligands and binding sites
- DUQ · (2S)-2-[(2,4-dioxopyrimidin-1-yl)methyl]-N-(2-hydroxyethyl)-4-trityloxy-butanamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.73 | 0.99 | 15 | empty |
| 2 | 411 | 0.69 | 0.81 | 41 | empty |
| 3 | 191 | 0.52 | 0.78 | 24 | SO4, DUQ |
| 4 | 175 | 0.49 | 0.77 | 22 | DUQ |
| 5 | 124 | 0.44 | 0.77 | 21 | DUQ |
Interfaces
3 interfaces between chains.
- A–B · 587 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 572 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2Y8C · Plasmodium falciparum dUTPase in complex with a trityl ligand · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8II92
- Elsewhere: RCSB PDB 2Y8C · PDBe 2Y8C · UniProt Q8II92
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